Variant report

Variant	rs2744300
Chromosome Location	chr6:25319234-25319235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25314690..25316229-chr6:25317879..25319908,2	K562	blood:
2	chr6:25304384..25306204-chr6:25317255..25319611,2	MCF-7	breast:
3	chr6:25314031..25316618-chr6:25318937..25320645,2	MCF-7	breast:
4	chr6:25318943..25320704-chr6:25326151..25329125,2	K562	blood:
5	chr6:25316945..25319715-chr6:25323364..25325803,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs2018839	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2064206	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2690041	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2690054	0.82[JPT][hapmap]
rs2690064	0.82[JPT][hapmap]
rs2690110	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2690112	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2690117	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690118	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2690132	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2690134	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2690135	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2744269	0.82[JPT][hapmap]
rs2744288	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2744289	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2744293	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2744294	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2744297	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721037	0.82[JPT][hapmap]
rs7741111	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25305000-25324400	Weak transcription	Left Ventricle	heart
2	chr6:25306600-25331400	Weak transcription	Spleen	Spleen
3	chr6:25310400-25319400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr6:25312000-25324200	Weak transcription	Esophagus	oesophagus
5	chr6:25312000-25324200	Weak transcription	Pancreas	Pancrea
6	chr6:25313400-25329800	Weak transcription	Primary T cells from cord blood	blood
7	chr6:25313600-25320200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:25313800-25322800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:25313800-25325800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr6:25313800-25326800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:25313800-25331400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:25314000-25325000	Weak transcription	Placenta	Placenta
13	chr6:25315400-25329600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:25315800-25324200	Weak transcription	Hela-S3	cervix
15	chr6:25316000-25320200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:25316000-25320400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr6:25316200-25320400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:25316200-25326800	Weak transcription	Gastric	stomach
19	chr6:25316400-25326600	Weak transcription	Fetal Kidney	kidney
20	chr6:25316600-25319600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:25316600-25324200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:25317200-25324200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:25317200-25324200	Weak transcription	Aorta	Aorta
24	chr6:25317400-25320200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:25317400-25320400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:25317400-25324000	Weak transcription	Fetal Intestine Large	intestine
27	chr6:25318000-25321600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr6:25318400-25319600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr6:25318400-25321200	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr6:25318400-25321200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:25318400-25321600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:25318600-25324200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:25318600-25324400	Weak transcription	Lung	lung
34	chr6:25319000-25319400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:25319000-25319400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:25319000-25319400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:25319000-25319600	Weak transcription	Small Intestine	intestine
38	chr6:25319000-25319800	Enhancers	Duodenum Mucosa	Duodenum
39	chr6:25319000-25320200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr6:25319000-25320200	Weak transcription	HSMMtube	muscle
41	chr6:25319000-25320400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:25319000-25320600	Enhancers	Fetal Intestine Small	intestine
43	chr6:25319000-25324200	Weak transcription	Ovary	ovary
44	chr6:25319000-25324200	Weak transcription	Right Atrium	heart
45	chr6:25319200-25320400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:25319200-25320600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr6:25319200-25324400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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